Gene expression profiling of a clonal isolate of oxaliplatin-resistant ovarian carcinoma cell line A2780/C10

The efficacy of platinum drugs in the treatment of cancer is often restricted by the acquisition of tumor cell resistance subsequent to treatment. To better understand mechanisms involved in this phenomenon, a clonal subline (A2780/C10B) isolated from an oxaliplatin-resistant human ovarian carcinoma cell line (A2780/C10) was developed, as reported previously. This cell line is 18-fold resistant to oxaliplatin and shows a 3-fold cross resistance to cisplatin. Here, we report on the gene expression analysis using Affymetrix HG-U95Av2 oligonucleotide arrays of cells in log phase growth from both the parental cell line and drug-resistant variant. Probe level analysis was perfomed using the model based expression index (dChip) and robust multichip average (RMA) methods. Genes that were differentially expressed between the two groups were identified using the significance analysis of microarrays (SAM) method with a minimum false discovery rate <1%. We identified 43 genes that were overexpressed, and 39 underexpressed in the drug-resistant cell line. Collagen VI (COL6A3) was overexpressed 62-fold and the most highly up-regulated gene. This finding is consistent with other published data based on serial analysis of gene expression (SAGE) profiling of cisplatin-resistant and sensitive ovarian carcinoma cells. Among the significant functional groups of overexpressed genes in our study were extracellular matrix genes (9 of 43) and those involved in signal transduction (7 of 43). Extracellular matrix genes included two matrix metalloproteinases (MMP3 and MMP12). Integrin alpha 1 (ITGA1) and WNT5A were also overexpressed. Genes that encode for extracellular matrix proteins were also among those found down-regulated in the resistant cell line. Several genes involved in the regulation of cell cycle and growth were found to be underexpressed, including the suppressor of cytokine signaling 2 (SOCS2), necdin (NDN), and glypicans (GPC3 and GPC4). The mRNA levels of six differentially expressed genes (COL6A3, MMP12, MMP3, WNT5A, NID, and HMGB2) were validated using real-time quantitative RT-PCR. The identification of these genes should aid in a better understanding of the pathways resulting in platinum drug resistance.